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A variational Bayesian method for similarity learning in non-rigid image registration

We provide the source code and the trained models used in the research presented at CVPR 2022. The model learns in an unsupervised way a data-specific similarity metric for atlas-based non-rigid image registration. The use of a learnt similarity metric parametrised as a neural network yields more accurate results than use of traditional similarity metrics, without a negative impact on the transformation smoothness or image registration speed.

Model

model

Neural network parametrising the similarity metric initialised to SSD. The model consists of a 3D U-Net encoder, which is initialised to the Dirac delta function and followed by a 1D convolutional layer. Feature maps output by the 3D U-Net are used to calculate a weighted sum returned by the aggregation layer. Before training, the output of the neural network approximates the value of SSD. We would like to thank Rhea Jiang from the Harvard Graduate School of Design for the figure.

Results

boxplot

Average surface distances and Dice scores calculated on subcortical structure segmentations when aligning images in the test split using the baseline and learnt similarity metrics. The learnt models show clear improvement over the baselines. We provide details on the statistical significance of the improvement in the paper.

Usage

Set-up

The experiments were run on a system with Ubuntu 20.04.4 and Python 3.8.6. To install the necessary Python libraries run the following command:

pip install requirements.txt

Training

Examples of json files with the model parameters can be found in the folder /configs. Use the following command to train a similarity metric:

CUDA_VISIBLE_DEVICES=<device_ids> python -m torch.distributed.launch --nproc_per_node=<no_gpus> train.py -c <path/to/config.json>

Testing

Use the following command to align images:

CUDA_VISIBLE_DEVICES=<device_id> python -m torch.distributed.launch --nproc_per_node=1 test.py -c <path/to/config.json> -r <path/to/checkpoint.pt>

Pre-trained models

For training and testing, we used brain MRI scans from the UK Biobank. Click on the links below to download the pre-trained models.

Model Baseline Learnt
SSD N/A 12 MB
LCC N/A 22 MB
VXM + SSD 1 MB 1 MB
VXM + LCC 1 MB 1 MB

Citation

If you use this code, please cite our paper.

Daniel Grzech, Mohammad Farid Azampour, Ben Glocker, Julia Schnabel, Nassir Navab, Bernhard Kainz, and Loïc Le Folgoc. A variational Bayesian method for similarity learning in non-rigid image registration. CVPR 2022.

@inproceedings{Grzech2022,
    author = {Grzech, Daniel and Azampour, Mohammad Farid and Glocker, Ben and Schnabel, Julia and Navab, Nassir and Kainz, Bernhard and {Le Folgoc}, Lo{\"{i}}c},
    title = {{A variational Bayesian method for similarity learning in non-rigid image registration}},
    booktitle = {CVPR},
    year = {2022}
}